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Free-energy calculations - Theoretical Biophysics Group

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References<br />

DIXIT, S. B.;CHIPOT, C. (2001): Can absolute free energies of association be estimated from molecular mechanical<br />

simulations ? The biotin–streptavidin system revisited, in: J. Phys. Chem. A, 105, S. 9795–9799.<br />

E, W.;REN, W.;VANDEN-EIJNDEN, E. (2005): Transition pathways in complex systems: Reaction coordinates,<br />

isocommittor surfaces, and transition tubes, in: Chemical Physics Letters, 413, S. 242–247.<br />

FENN, J. B.;MANN, M.;MENG, C. K.;WONG, S. F.;WHITEHOUSE, C. M. (1989): Electrospray ionization for mass<br />

spectrometry of large biomolecules, in: Science, 246, S. 64–71.<br />

FLYVBJERG, H.;PETERSEN, H. G. (1989): Error estimates on averages of correlated data, in: J. Chem. Phys., 91, S.<br />

461–466.<br />

GAO, J.;KUCZERA, K.;TIDOR, B.;KARPLUS, M. (1989): Hidden thermodynamics of mutant proteins: A molecular dynamics<br />

analysis, in: Science, 244, S. 1069–1072.<br />

GILSON, M. K.;GIVEN, J. A.;BUSH, B. L.;MCCAMMON, J. A. (1997): The statistical–thermodynamic basis for computation<br />

of binding affinities: A critical review, in: Biophys. J., 72, S. 1047–1069.<br />

HAHN, A. M.;THEN, H. (2009): Characteristic of Bennett’s acceptance ratio method, in: Phys. Rev. E Stat. Nonlin. Soft<br />

Matter Phys., 80, S. 031.111.<br />

HÉNIN, J.;CHIPOT, C. (2004): Overcoming free <strong>energy</strong> barriers using unconstrained molecular dynamics simulations, in: J.<br />

Chem. Phys., 121, S. 2904–2914.<br />

HERMANS, J.;WANG, L. (1997): Inclusion of loss of translational and rotational freedom in theoretical estimates of free<br />

energies of binding. Application to a complex of benzene and mutant T4 lysozyme, in: J. Am. Chem. Soc., 119, S.<br />

2707–2714.<br />

HUMMER, G.;PRATT, L.;GARCIA, A. E. (1996): <strong>Free</strong> <strong>energy</strong> of ionic hydration, in: J. Phys. Chem., 100, S. 1206–1215.<br />

HÜNENBERGER, P. H.;MCCAMMON, J. A. (1999): Ewald artifacts in computer simulations of ionic solvation and ion–ion<br />

interactions: A continuum electrostatics study, in: J. Chem. Phys., 110, S. 1856–1872.<br />

IZRAILEV, S.;STEPANIANTS, S.;ISRALEWITZ, B.;KOSZTIN, D.;LU, H.;MOLNAR, F.;WRIGGERS, W.;SCHULTEN, K. (1998):<br />

Steered molecular dynamics, in: DEUFLHARD, P.;HERMANS, J.;LEIMKUHLER, B.;MARK, A. E.;SKEEL, R.;REICH, S.<br />

(Hrsg.), Computational molecular dynamics: Challenges, methods, ideas, Bd. 4vonLecture Notes in Computational<br />

Science and Engineering, S. 39–65, Springer Verlag, Berlin.<br />

JARZYNSKI, C. (1997): Nonequilibrium equality for free <strong>energy</strong> differences, in: Phys. Rev. Lett., 78, S. 2690–2693.<br />

JORGENSEN, W. L.;RAVIMOHAN, C. (1985): Monte Carlo simulation of differences in free energies of hydration, in: J.<br />

Chem. Phys., 83, S. 3050–3054.<br />

Chris Chipot <strong>Free</strong>-<strong>energy</strong> <strong>calculations</strong>

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